GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Sinorhizobium meliloti 1021

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate SMc04093 SMc04093 acetyl-CoA synthetase

Query= reanno::pseudo5_N2C3_1:AO356_18695
         (651 letters)



>FitnessBrowser__Smeli:SMc04093
          Length = 649

 Score =  885 bits (2286), Expect = 0.0
 Identities = 423/638 (66%), Positives = 500/638 (78%), Gaps = 3/638 (0%)

Query: 7   YPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSFDDHHVD 66
           YPV       TL D ATY   Y++SV +P+ FW E  KR++W +P+T VK TSF+   V 
Sbjct: 6   YPVLEAAKNRTLLDNATYLEWYRESVADPEKFWGEHGKRIEWFEPYTKVKNTSFEGD-VS 64

Query: 67  IKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKFANALRG 126
           IKWF DG  NVSYNC+DRHL   G++ AIIWEGD+P   + ITY EL+++VC+ AN L+ 
Sbjct: 65  IKWFEDGLTNVSYNCIDRHLKTHGEKTAIIWEGDNPYLDKKITYNELYDKVCRLANVLKE 124

Query: 127 QDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSKVVITA 186
           Q V +GD VTIYMPMIPEA  AMLAC RIGAIHSVVFGGFSPEALAGRI+DC+S  VIT 
Sbjct: 125 QGVKKGDRVTIYMPMIPEAAYAMLACARIGAIHSVVFGGFSPEALAGRIVDCESTFVITC 184

Query: 187 DEGVRAGKKIPLKANVDDAL--TNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDLMKVA 244
           DEGVR GK + LK N D A+     +  ++ KV+V +RT G + W   RD+WY      A
Sbjct: 185 DEGVRGGKPVALKENTDTAIDIAARQHVTVSKVLVVRRTGGKVGWAPGRDLWYHQETAAA 244

Query: 245 GTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEVYWCT 304
              C P++M AE+ LFILYTSGSTGKPKGV HTT GYL+YA++TH+ VFDY+ G++YWCT
Sbjct: 245 EPHCPPEKMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYASMTHQYVFDYQDGDIYWCT 304

Query: 305 ADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTAIRAM 364
           ADVGWVTGHSYIVYGPLAN ATTL+FEGVPN+PD  R  +V+DKHKV+I YTAPTAIR++
Sbjct: 305 ADVGWVTGHSYIVYGPLANAATTLMFEGVPNFPDAGRFWEVVDKHKVNIFYTAPTAIRSL 364

Query: 365 MASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGGVLIS 424
           M +G   V+ +  SSLRLLG+VGEPINPEAW+WYY  VG ERCP+VDTWWQTETGG+LI+
Sbjct: 365 MGAGDDFVKRSSRSSLRLLGTVGEPINPEAWEWYYHVVGDERCPVVDTWWQTETGGILIT 424

Query: 425 PLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGDHDRF 484
           PLPGAT LKPGSATRPFFGV P +VD+ G +++GAA+GNL I DSWPGQ RT+YGDH+RF
Sbjct: 425 PLPGATDLKPGSATRPFFGVQPQIVDSDGKVVDGAADGNLCITDSWPGQMRTVYGDHERF 484

Query: 485 VDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHPKVAE 544
           + TYF T+ G YFTGDG RRDEDGYYWITGRVDDVLNVSGHR+GTAE+ESA+V+H  V+E
Sbjct: 485 IQTYFSTYKGKYFTGDGCRRDEDGYYWITGRVDDVLNVSGHRLGTAEVESALVSHNLVSE 544

Query: 545 AAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAPGLPK 604
           AAVVG PH IKGQGIY YV+L AGE   + LR  L   VR EIGPIA+PD IQ+APGLPK
Sbjct: 545 AAVVGYPHPIKGQGIYCYVSLMAGEVGDDELRQALVKHVRSEIGPIATPDKIQFAPGLPK 604

Query: 605 TRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLI 642
           TRSGKIMRRILRKIA  ++  LGD STLADPGVV  LI
Sbjct: 605 TRSGKIMRRILRKIAEDDFGSLGDTSTLADPGVVDDLI 642


Lambda     K      H
   0.318    0.135    0.418 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 1468
Number of extensions: 72
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 651
Length of database: 649
Length adjustment: 38
Effective length of query: 613
Effective length of database: 611
Effective search space:   374543
Effective search space used:   374543
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)

Align candidate SMc04093 SMc04093 (acetyl-CoA synthetase)
to HMM TIGR02188 (acs: acetate--CoA ligase (EC 6.2.1.1))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR02188.hmm
# target sequence database:        /tmp/gapView.15960.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02188  [M=629]
Accession:   TIGR02188
Description: Ac_CoA_lig_AcsA: acetate--CoA ligase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
          0 1034.6   0.0          0 1034.4   0.0    1.0  1  lcl|FitnessBrowser__Smeli:SMc04093  SMc04093 acetyl-CoA synthetase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc04093  SMc04093 acetyl-CoA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1034.4   0.0         0         0       4     628 ..      20     643 ..      17     644 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1034.4 bits;  conditional E-value: 0
                           TIGR02188   4 leeykelyeeaiedpekfwaklakeelewlkpfekvldeslep..kvkWfedgelnvsyncvdrhvekrkdkvai 76 
                                         + +y e+y+e+++dpekfw++++k ++ew++p++kv+++s+e   ++kWfedg +nvsync+drh++++ +k+ai
  lcl|FitnessBrowser__Smeli:SMc04093  20 NATYLEWYRESVADPEKFWGEHGK-RIEWFEPYTKVKNTSFEGdvSIKWFEDGLTNVSYNCIDRHLKTHGEKTAI 93 
                                         57899*******************.5***************987899**************************** PP

                           TIGR02188  77 iwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGfsae 151
                                         iwegd++    +k+tY+el+++vcrlanvlke+Gvkkgdrv+iY+pmipea++amlacaRiGa+hsvvf+Gfs+e
  lcl|FitnessBrowser__Smeli:SMc04093  94 IWEGDNPYL-DKKITYNELYDKVCRLANVLKEQGVKKGDRVTIYMPMIPEAAYAMLACARIGAIHSVVFGGFSPE 167
                                         *****9996.9**************************************************************** PP

                           TIGR02188 152 alaeRivdaeaklvitadeglRggkvielkkivdealekaee...svekvlvvkrtgeevaewkegrDvwweelv 223
                                         ala Rivd+e+ +vit deg+Rggk ++lk+++d a++ a +   +v+kvlvv+rtg +v  w  grD+w+++++
  lcl|FitnessBrowser__Smeli:SMc04093 168 ALAGRIVDCESTFVITCDEGVRGGKPVALKENTDTAIDIAARqhvTVSKVLVVRRTGGKVG-WAPGRDLWYHQET 241
                                         ************************************9876554579*************76.************* PP

                           TIGR02188 224 ekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGhsY 298
                                         +  a+ +c+pek+++edplfiLYtsGstGkPkGvlhttgGyl++a++t++yvfd++d+di+wCtaDvGWvtGhsY
  lcl|FitnessBrowser__Smeli:SMc04093 242 AA-AEPHCPPEKMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYASMTHQYVFDYQDGDIYWCTADVGWVTGHSY 315
                                         *5.************************************************************************ PP

                           TIGR02188 299 ivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepi 373
                                         ivygPLan attl+fegvp++pda+rfwev++k+kv+ifYtaPtaiR+lm +g+++vk+ ++sslr+lg+vGepi
  lcl|FitnessBrowser__Smeli:SMc04093 316 IVYGPLANAATTLMFEGVPNFPDAGRFWEVVDKHKVNIFYTAPTAIRSLMGAGDDFVKRSSRSSLRLLGTVGEPI 390
                                         *************************************************************************** PP

                           TIGR02188 374 npeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeveeeeeggv 448
                                         npeaweWyy+vvG+e+cp+vdtwWqtetGgilitplpg at+lkpgsat+P+fG+++++vd++gk v+  ++ g 
  lcl|FitnessBrowser__Smeli:SMc04093 391 NPEAWEWYYHVVGDERCPVVDTWWQTETGGILITPLPG-ATDLKPGSATRPFFGVQPQIVDSDGKVVDGAAD-GN 463
                                         **************************************.6***************************98777.79 PP

                           TIGR02188 449 LvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvs 523
                                         L+i+++wP+++rt+ygd+erf++tYf+++kg yftGDg+rrd+dGy+wi+GRvDdv+nvsGhrlgtae+esalvs
  lcl|FitnessBrowser__Smeli:SMc04093 464 LCITDSWPGQMRTVYGDHERFIQTYFSTYKGKYFTGDGCRRDEDGYYWITGRVDDVLNVSGHRLGTAEVESALVS 538
                                         *************************************************************************** PP

                           TIGR02188 524 heavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvveelPktRsGkimR 598
                                         h+ v+eaavvg+p+ ikg+ i+++v l++g+  d+ el++ l k+vr+eigpia+pdki++++ lPktRsGkimR
  lcl|FitnessBrowser__Smeli:SMc04093 539 HNLVSEAAVVGYPHPIKGQGIYCYVSLMAGEVGDD-ELRQALVKHVRSEIGPIATPDKIQFAPGLPKTRSGKIMR 612
                                         *****************************999999.5************************************** PP

                           TIGR02188 599 Rllrkiaege.ellgdvstledpsvveelke 628
                                         R+lrkiae++  +lgd+stl+dp vv++l++
  lcl|FitnessBrowser__Smeli:SMc04093 613 RILRKIAEDDfGSLGDTSTLADPGVVDDLIA 643
                                         ***************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (649 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 12.77
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory